R/read.cls.R

In jhart99/gseasier: Run the GSEA java pacakage from inside R

# Copyright ---------------------------------------------------------------
# 2018 The Scripps Research Institute Author: Jonathan Ross Hart

# Author ------------------------------------------------------------------
# Jonathan Ross Hart(jonathan@jonathanrosshart.com)

# Description -------------------------------------------------------------
# A demonstration of the gene signature overlap routines.

# Input -------------------------------------------------------------------
# msigdb formatted gmt files or yuor own gmt formatted gene sets

# Methods -------------------------------------------------

# Outputs -------------------------------------------------

# a table of comparisons between two sets of gene sets with odds ratios and
# p.values

# Library imports ---------------------------------------------------------

# acquire the msigdb files from Broad directly at
# http://software.broadinstitute.org/gsea/downloads.jsp

# this part will work with either set of genes.  Meaning you can use entrez ids
# or gene names as you prefer.


#' Title
#'
#' @param filename
#'
#' @return
#' @export
#'
#' @examples
read.cls <- function(filename) {
  file.handle <- file(filename, "r")
  cls.in <- readLines(file.handle, n = 3, warn = F)
  labels <- unlist(strsplit(cls.in[3], " "))
  close(file.handle)
  factor(labels)
}